bdarcus:

Many, many reasons. The reason it involves PDFs is that:
1. no other format supports all the features I want
2. I want a single interface for all of my annotation, so that the annotation experience is very seamless, and converting PDF to html is not practical, nor is there some third format that I could convert all documents to, nor is there some suitable annotation program which uses some other *set* of formats that I could covert everything to.

The reason the system is 'involved' is that I want to be able to do everything I do on paper, and then some:

- handwriting. This should be a no-brainer but very few programs have proper ink support-bluebeam's the only serious option for PDFs. I read a lot of mathematical documents and insert pages of lined paper for doing the exercises right there in the book, and I also jot notes in predicate logic regardless of the sort of document I'm reading. Also, scribbling a little diagram in a margin is a tried-and-true aid to understanding for all sorts of subject matters.

- highlight. physical highlighters were an instant hit as soon as they were invented, it seems. having highlights gives each page a striking appearance which aids memory and rapid recall of the page's content.

- various colors for highlighters. the distinctiveness of the page is further enhanced by having various colors--I use:
1 - grey for structural remarks like 'Firstly' or 'Conversely'
2 - ice blue for passages 'put on ice' (more on this below)
3 - yellow for general salience
4 - deep blue for 'quotable' passages
5 - red for disagreement
6 - orange for 'dubious' passages (they're 'almost' red)
7 - green for agreement
8 - pink for 'funny' passages
9 - purple for 'strange' passages

The passages I 'put on ice' are things I am skipping, or didn't understand, but will go back to, or things that I have a question to ask someone about--basically things marked for further processing in a text I'm otherwise done with--this is great because I can quickly generate a list of all ice blue items. With these colors a quick glance is often sufficient to recall a page's content

- hotkeys for highlighters. It may strike you that such a system is too complicated--and it would be, with physical highlighters, but in bluebeam I just press the number listed above (those digits have mnemonic significance too, actually)--it's seamless enough that I don't even think about what I'm doing now (unless I'm stuck in some other program, bah!)

- popup notes. typing remarks is a great tool for keeping ideas close to their source--counterarguments and so on are easily accessible on a re-reading years later. Normal 'note-taking' would require me to jot down page numbers and so-on,but why? (The only problem with bluebeam here is that it doesn't support unicode meaning I can't type the logical symbols I type using a script in other programs)

- heirarchical bookmarks. PDF bookmarks are a great way to create an outline of a document, plot, or argument, because then you can click on any part of the outline to go straight to that part of the text. The interface is also fairly seamless since you can highlight text, such as a header or short quote, and press a hotkey to have that text copied into a new bookmark. The ability to expand/collapse outlines also obviously gives functionality superior to paper outlines. My only complaint is that bluebeam, unlike acrobat, won't wrap long lines, forcing you to use very short bookmarks, and there's also no good keyboard shortcuts for indenting/outdenting/reordering. It woudl also be nice to be able to quickly copy such bookmarks into a more free-form document embedded in the PDF, so that one could scribble on the outline, or add extra text which is not a link, or adjust text formatting, but I've never seen anything like this.

- i also have 'weak' versions of all the highlight colours that involve handwritten ink, or special underline annotations, for instance a squiggly underline, or a tilde in the margin, is a weak version of the orange highlight, and an x or strikethrough is a weak red, a question mark is one weak form of ice blue, and so on. exclamation point is basically weak purple. I use ink for these because they stand out less, and are not searchable by category--these are basically what I used to scribble on paper documents for years before I switched to PDF.


This is all just an enhanced version of normal pencil-and-paper note-taking, involving:
- freeform writing on the document
- highlighting (multicolor)
- constructing outlines
- composing extended notes (here, in pop-up notes)
- doing exercises (for math problems)
- collecting quotations (using the blue highlight, or other colors)

Any software solution *MUST* support all of this if it's ever to replace pencil-and-paper completely--bluebeam's the only solution for this at the moment.

Also interested in this... any news?

I posted a few potentially useful tools for implementation of HTML to PDF conversion in this thread. https://forums.zotero.org/discussion/81185/feature-request-optionally-save-web-pages-as-pdf-and-a-list-of-tools-that-might-help